I know what you're saying. We'll have 100+ sites running on multisite within 12 months. Each site has it's own domain, IP, and SSL certificate. Perhaps you can look into an SSL wildcard certificate and use subdomains. My annual domain costs will run in the $20k+ range but it scales.

I have one site that is password protected. I just tweaked the system a tad on login... I also modified multisite to keep customer lists and baskets seperate for each site. Fairly simple with the componentized coding of zen-cart.